Submissions for variant NM_000152.5(GAA):c.2580C>T (p.Asp860=)

gnomAD frequency: 0.00459  dbSNP: rs61736894

Total submissions: 9

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Eurofins Ntd Llc (ga)	RCV000314439	SCV000332714	benign	not specified	2015-07-30	criteria provided, single submitter	clinical testing
GeneDx	RCV000314439	SCV000522329	likely benign	not specified	2017-09-05	criteria provided, single submitter	clinical testing	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Invitae	RCV001001755	SCV000626582	benign	Glycogen storage disease, type II	2024-01-31	criteria provided, single submitter	clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	RCV001001755	SCV001159367	benign	Glycogen storage disease, type II	2022-07-08	criteria provided, single submitter	clinical testing
Illumina Laboratory Services, Illumina	RCV001001755	SCV001285668	likely benign	Glycogen storage disease, type II	2018-01-13	criteria provided, single submitter	clinical testing	This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000314439	SCV001361268	benign	not specified	2019-03-11	criteria provided, single submitter	clinical testing	Variant summary: GAA c.2580C>T alters a non-conserved nucleotide resulting in a synonymous change. 5/5 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 0.0014 in 263280 control chromosomes, predominantly at a frequency of 0.015 within the African subpopulation in the gnomAD database. The observed variant frequency within African control individuals in the gnomAD database is approximately 4-folds higher than the estimated maximal expected allele frequency for a pathogenic variant in GAA causing Glycogen Storage Disease, Type 2 (Pompe Disease) phenotype (0.0042), strongly suggesting that the variant is a benign polymorphism found primarily in populations of African origin. To our knowledge, no occurrence of c.2580C>T in individuals affected with Glycogen Storage Disease, Type 2 (Pompe Disease) and no experimental evidence demonstrating its impact on protein function have been reported. Four ClinVar submission from clinical diagnostic laboratories (evaluation after 2014) cite the variant twice as likely benign and twice as benign. Based on the evidence outlined above, the variant was classified as benign.
Ambry Genetics	RCV002429213	SCV002740369	likely benign	Cardiovascular phenotype	2022-05-17	criteria provided, single submitter	clinical testing	This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Mayo Clinic Laboratories, Mayo Clinic	RCV000675249	SCV000800896	likely benign	not provided	2017-04-13	no assertion criteria provided	clinical testing
Natera, Inc.	RCV001001755	SCV002094470	likely benign	Glycogen storage disease, type II	2019-12-04	no assertion criteria provided	clinical testing